Fix how we structure the run notebook rules. #1384
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With this change, one can just run `make notebooks/py/smFISH.py` or `make smFISH.py`. For the examples in `docs/source/_static/data_processing_examples/`, we can also directly invoke them, i.e., `make 3d_smFISH.py`. Also, we run all notebooks with ipython instead of python now.
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ttung
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This should unbreak the cronjob. I think I broke this in #1384. Whoops!
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This should unbreak the cronjob. I think I broke this in #1384. Whoops!
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Jul 30, 2019
In #1384, I made it such that someone could run `make notebooks/py/xxxx.py` and run the notebook. Unfortunately, that created a dependency between the rule that regenerated the .ipynb file and the notebook running rule. This is not desirable, as regenerating the .ipynb files take forever now. This PR breaks that dependency. The idea is that the notebook regeneration process is so lightweight that we don't really need to examine the mtimes, and just do it blindly. Test: make -j validate-ipynb does not run the notebooks
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In #1384, I made it such that someone could run `make notebooks/py/xxxx.py` and run the notebook. Unfortunately, that created a dependency between the rule that regenerated the .ipynb file and the notebook running rule. This is not desirable, as regenerating the .ipynb files take forever now. This PR breaks that dependency. The idea is that the notebook regeneration process is so lightweight that we don't really need to examine the mtimes, and just do it blindly. Test: make -j validate-ipynb does not run the notebooks
ttung
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In #1384, I made it such that someone could run `make notebooks/py/xxxx.py` and run the notebook. Unfortunately, that created a dependency between the rule that regenerated the .ipynb file and the notebook running rule. This is not desirable, as regenerating the .ipynb files take forever now. This PR breaks that dependency. The idea is that the notebook regeneration process is so lightweight that we don't really need to examine the mtimes, and just do it blindly. Test: make -j validate-ipynb does not run the notebooks
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With this change, one can just run
make notebooks/py/smFISH.pyAlso, we run all notebooks with ipython instead of python now.